Several simple improvements to core functionality

1) Adds 'add_noise' option (defaults to true)
2) Better checking of Writer for if all glitch parameters have the same
length (avoid strange errors)
3) Fixes issue in which the tqdm ignore command was itself ignored

pyfstat/core.py

@@ -13,9 +13,8 @@ import lal
 import lalpulsar
 
 import helper_functions
-tqdm = helper_functions.set_up_optional_tqdm()
 helper_functions.set_up_matplotlib_defaults()
-args = helper_functions.set_up_command_line_arguments()
+args, tqdm = helper_functions.set_up_command_line_arguments()
 earth_ephem, sun_ephem = helper_functions.set_up_ephemeris_configuration()
 
 
@@ -672,7 +671,7 @@ class Writer(BaseSearchClass):
                  delta_F2=0, tref=None, F0=30, F1=1e-10, F2=0, Alpha=5e-3,
                  Delta=6e-2, h0=0.1, cosi=0.0, psi=0.0, phi=0, Tsft=1800,
                  outdir=".", sqrtSX=1, Band=4, detector='H1',
-                 minStartTime=None, maxStartTime=None):
+                 minStartTime=None, maxStartTime=None, add_noise=False):
         """
         Parameters
         ----------
@@ -701,19 +700,25 @@ class Writer(BaseSearchClass):
 
         for d in self.delta_phi, self.delta_F0, self.delta_F1, self.delta_F2:
             if np.size(d) == 1:
-                d = [d]
+                d = np.atleast_1d(d)
         self.tend = self.tstart + self.duration
         if self.minStartTime is None:
             self.minStartTime = self.tstart
         if self.maxStartTime is None:
             self.maxStartTime = self.tend
-        if self.dtglitch is None or self.dtglitch == self.duration:
+        if self.dtglitch is None or all(self.dtglitch == self.duration):
             self.tbounds = [self.tstart, self.tend]
         elif np.size(self.dtglitch) == 1:
-            self.tbounds = [self.tstart, self.tstart+self.dtglitch, self.tend]
+            self.dtglitch = np.array(dtglitch)
+            self.tbounds = np.concatenate((
+                [self.tstart], self.tstart+self.dtglitch, [self.tend]))
         else:
-            self.tglitch = self.tstart + np.array(self.dtglitch)
-            self.tbounds = [self.tstart] + list(self.tglitch) + [self.tend]
+            self.dtglitch = np.array(dtglitch)
+            self.tglitch = self.tstart + self.dtglitch
+            self.tbounds = np.concatenate((
+                [self.tstart], self.tglitch, [self.tend]))
+
+        self.check_inputs()
 
         if os.path.isdir(self.outdir) is False:
             os.makedirs(self.outdir)
@@ -736,6 +741,16 @@ class Writer(BaseSearchClass):
         self.sftfilepath = '{}/{}'.format(self.outdir, self.sftfilename)
         self.calculate_fmin_Band()
 
+    def check_inputs(self):
+        self.minStartTime = int(self.minStartTime)
+        self.maxStartTime = int(self.maxStartTime)
+        shapes = np.array([np.shape(x) for x in [self.delta_phi, self.delta_F0,
+                                                 self.delta_F1, self.delta_F2]]
+                          )
+        if not np.all(shapes == shapes[0]):
+            raise ValueError('all delta_* must be the same shape: {}'.format(
+                shapes))
+
     def make_data(self):
         ''' A convienience wrapper to generate a cff file then sfts '''
         self.make_cff()
@@ -865,6 +880,7 @@ transientTauDays={:1.3f}\n""")
         cl.append('--outSFTdir="{}"'.format(self.outdir))
         cl.append('--outLabel="{}"'.format(self.label))
         cl.append('--IFOs="{}"'.format(self.detector))
+        if self.add_noise:
             cl.append('--sqrtSX="{}"'.format(self.sqrtSX))
         if self.minStartTime is None:
             cl.append('--startTime={:10.9f}'.format(float(self.tstart)))

pyfstat/helper_functions.py

@@ -45,6 +45,8 @@ def set_up_command_line_arguments():
     if args.quite or args.no_interactive:
         def tqdm(x, *args, **kwargs):
             return x
+    else:
+        tqdm = set_up_optional_tqdm()
     logger = logging.getLogger()
     logger.setLevel(logging.DEBUG)
     stream_handler = logging.StreamHandler()
@@ -55,7 +57,7 @@ def set_up_command_line_arguments():
     stream_handler.setFormatter(logging.Formatter(
         '%(asctime)s %(levelname)-8s: %(message)s', datefmt='%H:%M'))
     logger.addHandler(stream_handler)
-    return args
+    return args, tqdm
 
 
 def set_up_ephemeris_configuration():